Abebe was 27 when he married 15-year-old Yewebdar Wolde-Giorgis on March 16, 1960. Although the marriage was arranged by his mother, Abebe was happy and they remained married for the rest of his life.
In July 1960, Abebe won his first marathon in Addis Ababa. A month later he won again in Addis Ababa with a time of 2:21:23, which was faster than the existing Olympic record held by Emil Zátopek. Niskanen entered Abebe Bikila and Abebe Wakgira in the marathon at the 1960 Rome Olympics, which would be run on September 10. In Rome, Abebe purchased new running shoes, but they did not fit well and gave him blisters. He consequently decided to run barefoot instead.
On December 13, 1960, while Haile Selassie was on a state visit to Brazil, Imperial Guard forces led by Mengistu began an unsuccessful coup and briefly proclaimed Selassie's eldest son Asfaw Wossen Taffari emperor. Fighting took place in the heart of Addis Ababa, shells detonated in the Jubilee Palace, and many of those closest to the emperor were killed. Although Abebe was not directly involved, he was briefly arrested and questioned. Mengistu was later hanged, and his forces (which included many members of the Imperial Guard) were killed in the fighting, arrested or fled.
Abebe ran the 1963 Boston Marathon—which was between his Olympic wins in 1960 and 1964—and finished fifth in 2:24:43. This was the only time in his competitive career that he completed an international marathon without winning. He and countryman Mamo Wolde, who finished 12th, had run together on record pace for 18 miles, until cold winds and the hills in Newton caused both to fall back. The race was won by Belgium's Aurele Vandendriessche in a course record 2:18:58. Abebe returned to Ethiopia and did not compete in another marathon until 1964 in Addis Ababa. He won that race in a time of 2:23:14.8.